Methods for bru_mapper objects

A bru_mapper sub-class implementation must provide an ibm_jacobian() method. If the model size 'n' and definition values 'values' are stored in the object itself, default methods are available (see Details). Otherwise the ibm_n() and ibm_values() methods also need to be provided.

Usage

# S3 method for bru_mapper_fm_mesh_2d
ibm_n(mapper, ...)

# S3 method for bru_mapper_fm_mesh_2d
ibm_values(mapper, ...)

# S3 method for bru_mapper_fm_mesh_2d
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_inla_mesh_2d
ibm_n(mapper, ...)

# S3 method for bru_mapper_inla_mesh_2d
ibm_values(mapper, ...)

# S3 method for bru_mapper_inla_mesh_2d
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_fm_mesh_1d
ibm_n(mapper, ...)

# S3 method for bru_mapper_fm_mesh_1d
ibm_values(mapper, ...)

# S3 method for bru_mapper_fm_mesh_1d
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_inla_mesh_1d
ibm_n(mapper, ...)

# S3 method for bru_mapper_inla_mesh_1d
ibm_values(mapper, ...)

# S3 method for bru_mapper_inla_mesh_1d
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_index
ibm_invalid_output(mapper, input, state, ...)

# S3 method for bru_mapper_index
ibm_jacobian(mapper, input, state, ...)

# S3 method for bru_mapper_taylor
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_taylor
ibm_n_output(mapper, input, ...)

# S3 method for bru_mapper_taylor
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_taylor
ibm_jacobian(mapper, ..., multi = FALSE)

# S3 method for bru_mapper_taylor
ibm_eval(mapper, input = NULL, state = NULL, ...)

# S3 method for bru_mapper_linear
ibm_n(mapper, ...)

# S3 method for bru_mapper_linear
ibm_values(mapper, ...)

# S3 method for bru_mapper_linear
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_matrix
ibm_n(mapper, ...)

# S3 method for bru_mapper_matrix
ibm_values(mapper, ...)

# S3 method for bru_mapper_matrix
ibm_jacobian(mapper, input, state = NULL, inla_f = FALSE, ...)

# S3 method for bru_mapper_factor
ibm_n(mapper, ...)

# S3 method for bru_mapper_factor
ibm_values(mapper, ...)

# S3 method for bru_mapper_factor
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_const
ibm_n(mapper, ...)

# S3 method for bru_mapper_const
ibm_values(mapper, ...)

# S3 method for bru_mapper_const
ibm_jacobian(mapper, input, ...)

# S3 method for bru_mapper_const
ibm_eval(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_scale
ibm_n(mapper, ..., state = NULL, n_state = NULL)

# S3 method for bru_mapper_scale
ibm_n_output(mapper, input, state = NULL, ..., n_state = NULL)

# S3 method for bru_mapper_scale
ibm_values(mapper, ..., state = NULL, n_state = NULL)

# S3 method for bru_mapper_scale
ibm_jacobian(mapper, input, state = NULL, ..., sub_lin = NULL)

# S3 method for bru_mapper_scale
ibm_eval(mapper, input, state = NULL, ..., sub_lin = NULL)

# S3 method for bru_mapper_aggregate
ibm_n(mapper, ..., input = NULL, state = NULL, n_state = NULL)

# S3 method for bru_mapper_aggregate
ibm_n_output(mapper, input = NULL, ...)

# S3 method for bru_mapper_aggregate
ibm_values(mapper, ..., state = NULL, n_state = NULL)

# S3 method for bru_mapper_aggregate
ibm_jacobian(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_aggregate
ibm_eval(mapper, input, state = NULL, ..., sub_lin = NULL)

# S3 method for bru_mapper_logsumexp
ibm_jacobian(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_logsumexp
ibm_eval(mapper, input, state = NULL, log = TRUE, ..., sub_lin = NULL)

# S3 method for bru_mapper_marginal
ibm_n(mapper, ..., state = NULL, n_state = NULL)

# S3 method for bru_mapper_marginal
ibm_n_output(mapper, input, state = NULL, ..., n_state = NULL)

# S3 method for bru_mapper_marginal
ibm_values(mapper, ..., state = NULL, n_state = NULL)

# S3 method for bru_mapper_marginal
ibm_jacobian(mapper, input, state = NULL, ..., reverse = FALSE)

# S3 method for bru_mapper_marginal
ibm_eval(mapper, input, state = NULL, ..., reverse = FALSE)

# S3 method for bru_mapper_pipe
ibm_n(mapper, ..., input = NULL, state = NULL)

# S3 method for bru_mapper_pipe
ibm_n_output(mapper, input, state = NULL, ..., n_state = NULL)

# S3 method for bru_mapper_pipe
ibm_values(mapper, ...)

# S3 method for bru_mapper_pipe
ibm_jacobian(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_pipe
ibm_eval(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_pipe
ibm_eval2(mapper, input, state = NULL, ...)

# S3 method for bru_mapper_pipe
ibm_simplify(mapper, input = NULL, state = NULL, ..., n_state = NULL)

# S3 method for bru_mapper_multi
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_multi
ibm_n_output(mapper, input, ...)

# S3 method for bru_mapper_multi
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_multi
ibm_is_linear(mapper, multi = FALSE, ...)

# S3 method for bru_mapper_multi
ibm_jacobian(
  mapper,
  input,
  state = NULL,
  inla_f = FALSE,
  multi = FALSE,
  ...,
  sub_A = NULL
)

# S3 method for bru_mapper_multi
ibm_linear(mapper, input, state, inla_f = FALSE, ...)

# S3 method for bru_mapper_multi
ibm_eval(
  mapper,
  input,
  state = NULL,
  inla_f = FALSE,
  ...,
  jacobian = NULL,
  pre_A = deprecated()
)

# S3 method for bru_mapper_multi
ibm_invalid_output(mapper, input, state, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_multi
[(x, i, drop = TRUE)

# S3 method for bru_mapper_multi
ibm_names(mapper)

# S3 method for bru_mapper_multi
ibm_names(mapper) <- value

# S3 method for bru_mapper_collect
ibm_n(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_collect
ibm_n_output(mapper, input, state = NULL, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_collect
ibm_values(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_collect
ibm_is_linear(mapper, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_collect
ibm_jacobian(
  mapper,
  input,
  state = NULL,
  inla_f = FALSE,
  multi = FALSE,
  ...,
  sub_lin = NULL
)

# S3 method for bru_mapper_collect
ibm_eval(
  mapper,
  input,
  state,
  inla_f = FALSE,
  multi = FALSE,
  ...,
  sub_lin = NULL
)

# S3 method for bru_mapper_collect
ibm_linear(mapper, input, state, inla_f = FALSE, ...)

# S3 method for bru_mapper_collect
ibm_invalid_output(mapper, input, state, inla_f = FALSE, multi = FALSE, ...)

# S3 method for bru_mapper_collect
[(x, i, drop = TRUE)

# S3 method for bru_mapper_collect
ibm_names(mapper)

# S3 method for bru_mapper_collect
ibm_names(mapper) <- value

# S3 method for bru_mapper_harmonics
ibm_n(mapper, inla_f = FALSE, ...)

# S3 method for bru_mapper_harmonics
ibm_jacobian(mapper, input, state = NULL, inla_f = FALSE, ...)

# S3 method for bru_mapper_mesh_B
ibm_n(mapper, ...)

# S3 method for bru_mapper_mesh_B
ibm_values(mapper, ...)

# S3 method for bru_mapper_mesh_B
ibm_jacobian(mapper, input, ...)

Arguments

mapper: A mapper S3 object, inheriting from bru_mapper.
...: Arguments passed on to other methods
input: The values for which to produce a mapping matrix
state: A vector of latent state values for the mapping, of length ibm_n(mapper, inla_f = FALSE)
inla_f: logical; when TRUE for ibm_n() and ibm_values(), the result must be compatible with the INLA::f(...) and corresponding INLA::inla.stack(...) constructions. For ibm_{eval,jacobian,linear}, the input interpretation may be different. Implementations do not normally need to do anything different, except for mappers of the type needed for hidden multicomponent models such as "bym2", which can be handled by bru_mapper_collect.
multi: logical; If TRUE (or positive), recurse one level into sub-mappers
n_state: integer giving the length of the state vector for mappers that have state dependent output size.
sub_lin: Internal, optional pre-computed sub-mapper information
log: logical; control log output. Default TRUE, see the ibm_eval() details for logsumexp mappers.
reverse: logical; control bru_mapper_marginal evaluation. Default FALSE. When TRUE, reverses the direction of the mapping, see details for marginal mappers.
sub_A: Internal; precomputed Jacobian matrices.
jacobian: For ibm_eval() methods, an optional pre-computed Jacobian, typically supplied by internal methods that already have the Jacobian.
pre_A: in favour of jacobian.
x: object from which to extract element(s)
i: indices specifying element(s) to extract
drop: logical; For [.bru_mapper_collect, whether to extract an individual mapper when i identifies a single element. If FALSE, a list of sub-mappers is returned (suitable e.g. for creating a new bru_mapper_collect object). Default: TRUE
value: a character vector of up to the same length as the number of mappers in the multi-mapper x

Value

[-indexing a bru_mapper_multi extracts a subset bru_mapper_multi object (for drop FALSE) or an individual sub-mapper (for drop TRUE, and i identifies a single element)

[-indexing a bru_mapper_collect extracts a subset bru_mapper_collect object (for drop FALSE) or an individual sub-mapper (for drop TRUE, and i identifies a single element)

The names() method for bru_mapper_collect returns the names from the sub-mappers list

Details

The ibm_eval.bru_mapper_taylor() evaluates linearised mapper information at the given state. The input argument is ignored, so that the usual argument order ibm_eval(mapper, input, state) syntax can be used, but also ibm_eval(mapper, state = state). For a mapper with a named jacobian list, the state argument must also be a named list. If state is NULL, all-zero is assumed.

For bru_mapper_scale, input values without a scale element are interpreted as no scaling.

For bru_mapper_aggregate, input should be a list with elements block and weights. block should be a vector of the same length as the state, or NULL, with NULL equivalent to all-1. If weights is NULL, it's interpreted as all-1.

For bru_mapper_logsumexp, input should be a list with elements block and weights. block should be a vector of the same length as the state, or NULL, with NULL equivalent to all-1. If weights is NULL, it's interpreted as all-1.

For bru_mapper_marginal, non-NULL input values are interpreted as a parameter list for qfun, overriding that of the mapper itself.

ibm_jacobian for bru_mapper_multi accepts a list with named entries, or a list with unnamed but ordered elements. The names must match the sub-mappers, see ibm_names.bru_mapper_multi(). Each list element should take a format accepted by the corresponding sub-mapper. In case each element is a vector, the input can be given as a data.frame with named columns, a matrix with named columns, or a matrix with unnamed but ordered columns.

ibm_invalid_output for bru_mapper_multi accepts a list with named entries, or a list with unnamed but ordered elements. The names must match the sub-mappers, see ibm_names.bru_mapper_multi(). Each list element should take a format accepted by the corresponding sub-mapper. In case each element is a vector, the input can be given as a data.frame with named columns, a matrix with named columns, or a matrix with unnamed but ordered columns.

ibm_jacobian for bru_mapper_collect accepts a list with named entries, or a list with unnamed but ordered elements. The names must match the sub-mappers, see ibm_names.bru_mapper_collect(). Each list element should take a format accepted by the corresponding sub-mapper. In case each element is a vector, the input can be given as a data.frame with named columns, a matrix with named columns, or a matrix with unnamed but ordered columns. When inla_f=TRUE and hidden=TRUE in the mapper definition, the input format should instead match that of the first, non-hidden, sub-mapper.

ibm_invalid_output for bru_mapper_collect accepts a list with named entries, or a list with unnamed but ordered elements. The names must match the sub-mappers, see ibm_names.bru_mapper_collect(). Each list element should take a format accepted by the corresponding sub-mapper. In case each element is a vector, the input can be given as a data.frame with named columns, a matrix with named columns, or a matrix with unnamed but ordered columns.

Functions

ibm_eval(bru_mapper_logsumexp): When log is TRUE (default), ibm_eval() for logsumexp returns the log-sum-weight-exp value. If FALSE, the sum-weight-exp value is returned.
ibm_eval(bru_mapper_marginal): When xor(mapper[["inverse"]], reverse) is FALSE, ibm_eval() for marginal returns qfun(pnorm(x), param), evaluated in a numerically stable way. Otherwise, evaluates the inverse qnorm(pfun(x, param)) instead.
ibm_simplify(bru_mapper_pipe): Constructs a simplified pipe mapper. For fully linear pipes, calls ibm_linear(). For partially non-linear pipes, replaces each sequence of linear mappers with a single bru_mapper_taylor() mapper, while keeping the full list of original mapper names, allowing the original input structure to be used also with the simplified mappers, since the taylor mappers are not dependent on inputs.
ibm_names(bru_mapper_multi): Returns the names from the sub-mappers list

Usage

Arguments

Value

Details

Functions

See also